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annotate krocus.xml @ 0:6a97c3a857d2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
author iuc
date Tue, 12 Mar 2024 10:45:51 +0000
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6a97c3a857d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
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1 <tool id="krocus" name="krocus" version="@VERSION@">
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2 <description>Multi-locus sequence typing (MLST) from uncorrected long reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">krocus</xref>
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8 </xrefs>
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9 <expand macro="requirements" />
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10 <expand macro="version_command" />
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11 <command detect_errors="exit_code"><![CDATA[
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12 krocus
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13 --output_file detected_mlst.tsv
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14 #if $opt_args.filtered_reads
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15 --filtered_reads_file filtered_reads.fq
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16 #end if
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17 --max_gap $opt_args.max_gap
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18 --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
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19 --margin $opt_args.margin
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20 --min_block_size $opt_args.min_block_size
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21 --min_fasta_hits $opt_args.min_fasta_hits
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22 --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
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23 --max_kmers $opt_args.max_kmers
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24 --print_interval $opt_args.print_interval
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25 --kmer $opt_args.kmer
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26 $opt_args.divisible_by_3
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27 $opt_args.verbose
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28 '$krocus_mlst_databases.fields.path' '$fastq'
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param name="fastq" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single read"/>
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33 <param label="Select a database" name="krocus_mlst_databases" type="select">
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34 <options from_data_table="krocus_mlst_databases">
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35 <validator message="No database is available" type="no_options" />
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36 </options>
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37 </param>
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38 <section name="opt_args" title="Optional Arguments">
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39 <param name="filtered_reads" type="boolean" truevalue="true" falsevalue="" checked="false" label="Save filtered reads ?"/>
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40 <param argument="--max_gap" type="integer" min="1" value="4" label="Maximum gap for blocks to be contigous, measured in
6a97c3a857d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
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41 multiples of the k-mer size" help="Default:4" />
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42 <param argument="--margin" type="integer" min="1" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
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43 <param argument="--min_block_size" type="integer" min="1" value="150" label="Minimum block size in bases" help="Default:150" />
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44 <param argument="--min_fasta_hits" type="integer" min="1" value="10" label="Minimum No. of kmers matching a read" help="Default:10" />
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45 <param argument="--min_kmers_for_onex_pass" type="integer" min="2" value="5" label="Minimum No. of kmers matching a read in 1st pass" help="Default:5" />
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46 <param argument="--max_kmers" type="integer" min="1" value="10" label="Dont count kmers occuring more than this many times" help="Default:10" />
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47 <param argument="--print_interval" type="integer" min="1" value="10" label="Print ST every this number of reads" help="(Default:500)" />
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48 <param argument="--kmer" type="integer" min="2" value="10" label="k-mer size" help="(Default:11)" />
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49 <param argument="--divisible_by_3" type="boolean" truevalue="--divisible_by_3" falsevalue="" checked="false" label="Genes which are not divisible by 3 are excluded" help="(Default:No)" />
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50 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on debugging" help="(Default:No)" />
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51 </section>
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52 </inputs>
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53
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54 <outputs>
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55 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Output" from_work_dir="detected_mlst.tsv"/>
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56 <data name="filtered_reads" format="fastq" label="${tool.name} on ${on_string}: Filtered reads" from_work_dir="filtered_reads.fq">
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57 <filter>opt_args['filtered_reads'] is True</filter>
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58 </data>
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59 </outputs>
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60
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61 <tests>
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62 <test expect_num_outputs="1">
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63 <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
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64 <param name="krocus_mlst_databases" value="mlst_db"/>
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65 <output name="output_file" ftype="tabular" file="mlst_output_pacbio.tsv" compare="sim_size" />
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66 </test>
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67 <test expect_num_outputs="2">
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68 <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
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69 <param name="filtered_reads" value="True" />
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70 <param name="krocus_mlst_databases" value="mlst_db"/>
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71 <output name="filtered_reads" ftype="fastq" file="filtered_reads.fq" compare="sim_size" />
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72 </test>
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73 </tests>
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74
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75 <help><![CDATA[
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76 Multi-locus sequence typing (MLST) from uncorrected long reads
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77
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78 Krocus can predict a sequence type directly from uncorrected long reads, and
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79 which was designed to consume read data as it is produced, providing results
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80 in minutes. It is the only tool which can do this from uncorrected long
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81 reads. We tested Krocus on over 600 samples sequenced with using long read
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82 sequencing technologies from PacBio and Oxford Nanopore. It provides
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83 sequence types on average within 90 seconds, with a sensitivity of 94% and
6a97c3a857d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
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84 specificity of 97%, directly from uncorrected raw sequence reads.
6a97c3a857d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
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85
6a97c3a857d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
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86 Documentation can be found at `<https://github.com/andrewjpage/krocus>`_.
6a97c3a857d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
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87 ]]>
6a97c3a857d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
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88 </help>
6a97c3a857d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
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89 <expand macro="citations"/>
6a97c3a857d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
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90 </tool>